CeleScope Report

Chemistry : For more information, see here.

Raw Reads : Total reads from FASTQ files.

Valid Reads : Reads pass filtering(filtered: reads without poly T, reads without linker, reads without correct barcode or low quality reads).

Q30 of Barcodes : Percent of barcode base pairs with quality scores over Q30.

Q30 of UMIs : Percent of UMI base pairs with quality scores over Q30.

Reads with Adapters : R2 reads with poly A(read-through adpaters) or sequencing adapters.

Reads Too Short : Reads with read length less than 20bp after trimming.

Reads Written : Reads pass filtering.

Base Pairs Processed : Total processed base pairs.

Base Pairs Quality-Trimmed : Bases pairs removed from the end of the read whose quality is smaller than the given threshold.

Base Pairs Written : Base pairs pass filtering.

Reads Mapped : R2 reads that successfully mapped to linker and tag-barcode.

Reads Unmapped Too Short : Unmapped R2 reads because read length < linker length + tag-barcode length.

Reads Unmapped Invalid Linker : Unmapped R2 reads because of too many mismatches in linker sequence.

Reads Unmapped Invalid Barcode : Unmapped R2 reads because of too many mismatches in tag-barcode sequence.

Mapped Reads in Cells : Mapped reads with scRNA-Seq cell barcode.

Median UMI per Cell : Median UMI per scRNA-Seq cell barcode.

Mean UMI per Cell : Mean UMI per scRNA-Seq cell barcode.